[R] Random covariate in survreg (Survival)

From: C. E. Timothy Paine <cetpaine_at_gmail.com>
Date: Sat 25 Mar 2006 - 05:23:02 EST


Dear R Listers-

I am attempting to analyse the survival of seeds in cages (exclosures) that differ in their permeability to rainforest mammals. Because I did not observe the moment of seed disappearance, my data is interval censored. This limits my options for analysis (as I understand it) to survreg, in the survival package. Because I repeated the experiment in 8 sites, I have a random covariate. Additionally, my analysis should properly be treated as a split-plot design, since seeds of all 15 species were sown into each exclosure. Survreg, it appears, cannot handle random predictor variables. Nor can survreg handle multiple error terms.

Please, can you advise me on a way forward? How can I extract survival functions for each species/treatment combination? I understand that I can avoid the split-plot issue by running separate analyses on each species. But I'd appreciate any direction on how to incorporate 'site', the random blocking variable.

Some code follows...
Surv.all<-Surv(data.raw$interval.start, data.raw$interval.end, data.raw$censor, type = "interval")
#this runs fine...

survreg.1<-survreg(Surv.all ~ species*trt, weights = freq, data = data.raw)
#this does not work...
survreg.2<-survreg(Surv.all ~ species*trt, random = ~ site, weights = freq, data = data.raw)

thanks in advance for your help!
tim

Running R version 2.2.1, 2005-12-20, on Mac OS 10.4.5



C. E. Timothy Paine
Dept. of Biological Sciences
107 Life Sciences Building
Louisiana State University
Baton Rouge, LA 70803

225-578-7567
cpaine3@lsu.edu

    650 species of rainforest trees...
    www.biology.lsu.edu/labpages/harmslab/tim



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